YAZB - BACSU - GREMLIN Contacts

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YAZB - Uncharacterized HTH-type transcriptional regulator YazB

UniProt:	O31417	Sequences: MEAEIWGRRIRAFRKLKGYTQEGFAKALGISVSILGEIERGNRLPSAAIIQDAADVLNISADELAPPEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	69 (59)
Sequences:	650 (585)
Seq/√Len:	76.2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_R	39_E	5.544	1.00
9_R	63_E	2.815	1.00
24_F	57_L	2.794	1.00
24_F	35_L	2.314	1.00
22_E	32_V	2.067	1.00
7_G	10_I	1.789	1.00
13_F	17_K	1.770	1.00
38_I	45_P	1.665	1.00
49_I	52_D	1.586	0.99
37_E	42_N	1.582	0.99
30_I	35_L	1.515	0.99
13_F	59_I	1.484	0.99
20_T	23_G	1.474	0.99
34_I	38_I	1.465	0.99
38_I	49_I	1.414	0.99
21_Q	36_G	1.405	0.99
27_A	56_V	1.393	0.99
13_F	57_L	1.338	0.98
30_I	38_I	1.324	0.98
51_Q	55_D	1.279	0.98
38_I	43_R	1.271	0.97
32_V	36_G	1.236	0.97
50_I	61_A	1.210	0.97
13_F	53_A	1.201	0.96
22_E	26_K	1.187	0.96
28_L	56_V	1.173	0.96
36_G	40_R	1.151	0.95
8_R	12_A	1.092	0.94
23_G	26_K	1.054	0.93
31_S	34_I	1.018	0.91
21_Q	32_V	1.014	0.91
54_A	61_A	0.983	0.90
59_I	64_L	0.952	0.88
17_K	58_N	0.940	0.88
7_G	14_R	0.866	0.83
26_K	48_A	0.829	0.80
38_I	50_I	0.815	0.79
33_S	37_E	0.793	0.77
7_G	39_E	0.791	0.77
24_F	53_A	0.780	0.76
21_Q	39_E	0.748	0.73
34_I	37_E	0.747	0.73
48_A	52_D	0.746	0.73
14_R	25_A	0.740	0.72
25_A	30_I	0.732	0.72
54_A	64_L	0.729	0.71
61_A	65_A	0.723	0.71
62_D	65_A	0.705	0.69
22_E	30_I	0.704	0.69
51_Q	61_A	0.702	0.68
14_R	19_Y	0.700	0.68
11_R	21_Q	0.692	0.67
25_A	35_L	0.677	0.66
10_I	24_F	0.675	0.65
21_Q	35_L	0.663	0.64
13_F	58_N	0.654	0.63
25_A	28_L	0.649	0.62
50_I	65_A	0.636	0.61
17_K	57_L	0.633	0.60
10_I	35_L	0.621	0.59
15_K	19_Y	0.618	0.59
23_G	27_A	0.613	0.58
31_S	37_E	0.613	0.58
16_L	25_A	0.611	0.58
28_L	35_L	0.611	0.58
11_R	15_K	0.600	0.56
33_S	42_N	0.595	0.56
30_I	49_I	0.591	0.55
54_A	60_S	0.590	0.55
45_P	50_I	0.587	0.55
47_A	58_N	0.581	0.54
50_I	60_S	0.577	0.53
9_R	54_A	0.567	0.52
11_R	39_E	0.565	0.52
18_G	44_L	0.562	0.52
60_S	63_E	0.557	0.51
41_G	48_A	0.551	0.50
51_Q	58_N	0.545	0.49
33_S	62_D	0.535	0.48
19_Y	39_E	0.534	0.48
44_L	53_A	0.531	0.48
36_G	42_N	0.531	0.48
44_L	47_A	0.526	0.47
10_I	53_A	0.519	0.46
13_F	24_F	0.513	0.45
14_R	21_Q	0.513	0.45
52_D	55_D	0.513	0.45
25_A	57_L	0.500	0.44

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3u3wA	2	0.9565	99.5	0.237	Contact Map
1y9qA	1	1	99.5	0.25	Contact Map
4yarA	2	1	99.5	0.258	Contact Map
4ndwA	2	0.9565	99.5	0.267	Contact Map
4ichA	2	0	99.4	0.281	Contact Map
3ivpA	2	1	99.4	0.282	Contact Map
4y42A	6	1	99.4	0.284	Contact Map
3zhiA	1	0.9275	99.4	0.286	Contact Map
4pu7B	2	0.913	99.4	0.286	Contact Map
2p5tA	2	0.0435	99.4	0.289	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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